July 07, 2021

How to manage psychological stress of hydrogeologists / numerical modelers?

July 07, 2021/ Saul Montoya

Over the time, we have seen numerical modeling as a great tool for the evaluation of the groundwater flow regime and we might have seen numerical modelers as high level professionals with strong analytical capabilities that can provide all the answers we need to proof that a project is sustainable or the accuracy of a predictive simulation. On a broad perspective we might have overestimated the numerical modeling exercise and sometimes deified numerical modelers, but by sure we haven’t seen them as humans.

July 02, 2021

How to insert and read Observation Points (OBS6) in Modflow 6 with Model Muse and Flopy - Tutorial

July 02, 2021/ Saul Montoya

Modflow 6 has a new approach in setting up observation points and it's essentially different to the previous versions. The OBS6 package works not only with heads and drawdowns but also with flows, so it's also possible to calibrate the model against baseflow or any other recorded flow from a boundary condition directly. We have created an applied case of the implementation of piezometers in a hillslope groundwater flow model in Modflow 6 and Model Muse. The tutorial covers all the steps related to the implementation of the observed points in Model Muse as well as the comparison among simulated and observed heads through scripts in Flopy.

June 24, 2021

How to install the Python geological modeling library Gempy in Windows with Debian and WSL

June 24, 2021/ Saul Montoya

Gempy is an open-source library for modeling geology written in Python. The library is capable of creating complex 3D geological models including structures, fault networks, and unconformities and it can be coupled with uncertainty analysis.

Due to the required packages and specific configuration the installation of Gempy is a challenge on Windows, we have developed an alternative installation process by the use of a Debian kernel under a Windows Subsystem for Linux. This tutorial shows the complete procedure to install Gempy from the Debian kernel setup to the review of the Gempy in Python.

June 21, 2021

How to create a point/line/polygon shapefile with Python and Fiona - Tutorial

June 21, 2021/ Saul Montoya

Storage, management and analysis of geospatial vector data as an ESRI shapefile is a common procedure of GIS and related professionals. The generation of these spatial files can be done not only on a desktop software but also by Python commands. We have created an applied example that shows the procedure in Python to create point, line, and polygon shapefiles from a csv file by the use of the Fiona library.

June 18, 2021

How to install Python geospatial libraries (Gdal, Fiona, Rasterio, etc) under a Conda Env in Windows

June 18, 2021/ Saul Montoya

Python is a great tool for spatial analysis and geomachine learning, however sometimes the Windows operating system presents some difficulties to install and run the bunch of Python libraries such as Gdal, Fiona, Geopandas, Rasterio. We are aware that most geoscientists, water resources specialists and related professionals work on Windows, therefore we are always in the search of new ways to get Python working with all its geospatial capabilities in every computer. We have created a tutorial that shows the installation process of the Python geospatial libraries in Windows by the use of a Conda environment; the process is simple on its steps, however the sequence and factors related to the package compatibility are important on the installation.

June 15, 2021

A place to find MODFLOW executables for any operating system: Windows, Mac or Linux

June 15, 2021/ Saul Montoya

A normal distribution of the core versions of MODFLOW as well as its variants, and Modflow-Based particle tracking and solute transport models includes not only the executables for Windows, but also the documentation, source code, test problems and other utility programs. Working with the multiple tools of Modflow implies a huge collection of files that aren’t useful for the simulation itself if you are working on Windows. Modelers working on Mac or Linux had to compile our executable by themselves.

June 03, 2021

How to extract centroid coordinates in QGIS with Field Calculator - Tutorial

June 03, 2021/ Saul Montoya

We did a simple procedure in QGIS but unknown to us that extracts the centroids of lines and polygons with Field Calculator commands inside the attribute table. The procedure is straightforward and does not involve the use of any intermediate layer.

June 02, 2021

How to install Postgresql and Postgis in Windows 10 with WSL and Debian - Tutorial

June 02, 2021/ Saul Montoya

The normal method to install Postgresql and Postgis requires the set up of several binaries and the workflow is usually on graphical user interfaces (GUI). We wanted to come with a way to install Postgresql and Postgis in Windows 10 while keeping the shell experience from Linux. This tutorial shows the procedure to install the database inside a Debian application (it could be Ubuntu as well) in Windows 10 that can actually be accessible from QGIS.

June 01, 2021

What we dont see in the development of open source software for groundwater modeling

June 01, 2021/ Saul Montoya

Usually we dedicate much time to developing tutorials and sometimes, just a few times, we actually write an article on this blog. Lately, our aim to discover and code is much greater than our impulse to give our opinion. This post is a special case where we write something without knowing if it is written because we are motivated or because there is something that needs to be written. In any case, writing this post doesn’t make us more free or happy... “Es macht uns nicht mehr zufrieden”... because we don´t know much about some things related to human nature.

May 28, 2021

5 tutorials for crop detection and vegetation delineation with Python and QGIS

May 28, 2021/ Saul Montoya

Over the last months we have researched the different tools in Python and QGIS available to recognize crops and vegetation as geospatial vector files. We have used a variety of techniques that range from machine learning algorithms with Scikit Learn and Scikit Image to just more innovative band combinations and reclassifications in QGIS. This article shows the summary of the tutorials produced so far that we are sure will be very helpful for GIS professionals and geoscientists.

May 26, 2021

Mixing groundwater and seawater geochemical modeling with Phreeqc and Python - Tutorial

May 26, 2021/ Saul Montoya

Phreeqc can solve geochemical simulations for a specific solution and simulations relying on previous results. We have developed a tutorial that goes through the Example 3 from the Phreeqc documentation in a stepwise approach to simulate groundwater, seawater, the mixing from both and cases regarding the equilibrium with calcite and dolomite. There is a Python class capable of running the input files and parse results incluided on the scripting part of the input files.

May 21, 2021

A geospatial Python class for crop recognition over drone orthophoto - Tutorial

May 21, 2021/ Saul Montoya

Spatial analysis and machine learning sometimes require massive coding in order to achieve decent results such as identifying plants from a drone orthophoto. We wanted to create a simple workflow for beginner and intermediate Python users to work with these libraries without much pain or frustration. This tutorial has the complete procedure to use a Python class that recognizes plants from an orthophoto based on sample points and creates intermediate plots and identifies plants as point shapefiles.

May 18, 2021

How to delineate crops from Drone Orthophotos with QGIS - Tutorial

May 18, 2021/ Saul Montoya

While doing research on machine learning algorithms for drone orthophotos we found that crops can be delineated with just standard QGIS with excellent performance. Based on the addition of the blue and red band divided by the green band we can have a new vegetation index where the most healthy crops have low index values (0-1.5) and the dry crops / barren soil have high values (more than 1.9). This tutorial shows the complete procedure on QGIS to perform the delineation from bean plants on a drone orthophoto with a resolution of 5cm.

May 14, 2021

How to make a geological map with QGIS - Tutorial

May 14, 2021/ Saul Montoya

This tutorial deals with the representation of geological information at regional scale from the Central Beaverhead Mountains, Idaho, US and creates a geological map through a series of processing and representation steps as:

Applying styles to geological units
Representation of contacts and normal / thrust faults

May 08, 2021

How to interpolate geospatial points to contours with Python and GDAL - Tutorial

May 08, 2021/ Saul Montoya

We have developed an alternative to a common procedure in GIS that is to create contours from a point shapefile but just with Python commands. By the use of Python and the GDAL library we can store this process into a function and perform contours from several point sets or different point queries.

May 05, 2021

How to download well info and groundwater levels from the NWIS server with Python - Tutorial

May 05, 2021/ Saul Montoya

We have developed an applied example to download information and groundwater levels for one well and multiple wells with Python and the dataretrieval package. The tutorial stores information and levels on a csv file an can be easily applied for streamflow and water quality data stored on the NWIS.

May 03, 2021

How to make a lake/reservoir volume-elevation curve with Python - Tutorial

May 03, 2021/ Saul Montoya

Python is a programming language capable of performing calculations for hydrological studies and water resources evaluations. We have done a tutorial for the volume-elevation curve determination of the lake Patillas in Puerto Rico with Python and numerical / spatial libraries as Numpy and Rasterio. Finally, results were compared to the volume-elevation curve form a USGS survey. The procedure was done this time for a lake, but can be easily applied to any reservoir or water body when the bottom elevation is available as a raster file.

April 29, 2021

How to make a lake bathymetric map with QGIS - Tutorial

April 29, 2021/ Saul Montoya

Bathymetric data requires some spatial processing to represent lake bottom elevation contours and lake depth. This tutorial shows the complete procedure to analyse a bathymetric survey on the Lake Patillas in Puerto Rico with QGIS to generate:

April 27, 2021

How to make a wind rose with Python - Tutorial

April 27, 2021/ Saul Montoya

Python is a useful tool for data analysis but also for data representation and as a graphic tool. This is an applied tutorial for the representation of a wind rose with Python from wind speed and direction stored on an Excel spreadsheet. The tutorial explores the options of the library to represent windroses as bars, boxes, polygons or contours.

April 15, 2021

Gypsum and Anhydrite solubility calculation with Phreeqc and Python - Tutorial

April 15, 2021/ Saul Montoya

Tutorial for the calculation of the solubility and thermodynamic stability of gypsum and anhydrite. The example simulates the dissolution of two minerals in a beaker at equilibrium, and the beaker is heated step-wise from 25ºC to 75ºC. Concentrations and saturation indices for the initial solution and the batch reaction are shown as Pandas dataframes and plotted as bar diagrams on a Jupyter Notebook. Finally a plot of the saturation index for anhydrite and gypsum with temperature is generated from an iteration over the batch reaction steps.

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